Continuity: During the scene on the lake, as Count Olaf is pushing Aunt Josephine's boat away, we cut to Lemony Snicket at his typewriter. On the paper in the typewriter can be seen the words, "...the Viper leapt...", a reference to an earlier scene in Uncle Monty's Reptile Room.

At the start of the wedding play, we see Olaf's actresses singing, "Nothing in the world..." and then the curtains behind them open. We then cut to a shot of Klaus sneaking away from the stage, but the curtains are closed (this goof is the side-effect of the cutting of an earlier sequence).

When Aunt Josephine is showing the children her photo album, one shot shows Violet turning the page with the aviation photo directly to the page with the group photo. In the next shots, however, she turns two more pages before coming upon the group picture.

When Count Olaf asks them why the children have not cooked him roast beef, he is seen standing on the ground in front of his acting troupe, but in the next shot, about a second later, he is shown jumping down from the table. This is due to cutting an extended scene where Olaf gets onto the table and ruins the dinner they have prepared.

When Violet and Klaus are pulling in the string with the elf head attached to it in order to try switching the train track over again Sunny is seen behind them facing forward and not moving. In the next cut, she is actively helping to pull the string back in herself.

During the leech attack, Violet and Klaus wave their arms in the air, signaling the nearby boat, and Violet's hair is down. When Count Olaf drives up in the boat, Violet's hair is up.

When the children enter Count Olaf's house for the first time, and Count Olaf is at the top of the stairs, he has no writing on the palms of his hands. Then when he walks down the stairs and is talking to the children, he has names and stick figures of the children on the palms of his hands.

When Count Olaf is saying goodbye to the kids his hand is on the car's door handle. Then we cut to a shot from inside the car and Count Olaf's hands are on the windowsill.